zcat BY4741-32C-GSM1661127/SRR1980072_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-32C-GSM1661127/SRR1980072_1.fastq.bam
zcat BY4741-32C-GSM1661127/SRR1980072_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-32C-GSM1661127/SRR1980072_2.fastq.bam
zcat BY4741-37C_rep1-GSM1661171/SRR1980116_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-37C_rep1-GSM1661171/SRR1980116_1.fastq.bam
zcat BY4741-37C_rep1-GSM1661171/SRR1980116_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-37C_rep1-GSM1661171/SRR1980116_2.fastq.bam
zcat BY4741-37C_rep2-GSM1661172/SRR1980117_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-37C_rep2-GSM1661172/SRR1980117_1.fastq.bam
zcat BY4741-37C_rep2-GSM1661172/SRR1980117_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-37C_rep2-GSM1661172/SRR1980117_2.fastq.bam
zcat BY4741-37C_rep3-GSM1661173/SRR1980118_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-37C_rep3-GSM1661173/SRR1980118_1.fastq.bam
zcat BY4741-37C_rep3-GSM1661173/SRR1980118_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-37C_rep3-GSM1661173/SRR1980118_2.fastq.bam
zcat BY4741-No_crosslinking-GSM1661128/SRR1980073_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-No_crosslinking-GSM1661128/SRR1980073_1.fastq.bam
zcat BY4741-No_crosslinking-GSM1661128/SRR1980073_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-No_crosslinking-GSM1661128/SRR1980073_2.fastq.bam
zcat BY4741-No_ligation-GSM1661129/SRR1980074_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-No_ligation-GSM1661129/SRR1980074_1.fastq.bam
zcat BY4741-No_ligation-GSM1661129/SRR1980074_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741-No_ligation-GSM1661129/SRR1980074_2.fastq.bam
zcat BY4741_rep10-GSM1661118/SRR1980063_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep10-GSM1661118/SRR1980063_1.fastq.bam
zcat BY4741_rep10-GSM1661118/SRR1980063_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep10-GSM1661118/SRR1980063_2.fastq.bam
zcat BY4741_rep11-GSM1661119/SRR1980064_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep11-GSM1661119/SRR1980064_1.fastq.bam
zcat BY4741_rep11-GSM1661119/SRR1980064_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep11-GSM1661119/SRR1980064_2.fastq.bam
zcat BY4741_rep12-GSM1661120/SRR1980065_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep12-GSM1661120/SRR1980065_1.fastq.bam
zcat BY4741_rep12-GSM1661120/SRR1980065_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep12-GSM1661120/SRR1980065_2.fastq.bam
zcat BY4741_rep13-GSM1661121/SRR1980066_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep13-GSM1661121/SRR1980066_1.fastq.bam
zcat BY4741_rep13-GSM1661121/SRR1980066_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep13-GSM1661121/SRR1980066_2.fastq.bam
zcat BY4741_rep14-GSM1661122/SRR1980067_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep14-GSM1661122/SRR1980067_1.fastq.bam
zcat BY4741_rep14-GSM1661122/SRR1980067_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep14-GSM1661122/SRR1980067_2.fastq.bam
zcat BY4741_rep15-GSM1661123/SRR1980068_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep15-GSM1661123/SRR1980068_1.fastq.bam
zcat BY4741_rep15-GSM1661123/SRR1980068_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep15-GSM1661123/SRR1980068_2.fastq.bam
zcat BY4741_rep16-GSM1661124/SRR1980069_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep16-GSM1661124/SRR1980069_1.fastq.bam
zcat BY4741_rep16-GSM1661124/SRR1980069_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep16-GSM1661124/SRR1980069_2.fastq.bam
zcat BY4741_rep17-GSM1661125/SRR1980070_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep17-GSM1661125/SRR1980070_1.fastq.bam
zcat BY4741_rep17-GSM1661125/SRR1980070_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep17-GSM1661125/SRR1980070_2.fastq.bam
zcat BY4741_rep18-GSM1661126/SRR1980071_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep18-GSM1661126/SRR1980071_1.fastq.bam
zcat BY4741_rep18-GSM1661126/SRR1980071_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep18-GSM1661126/SRR1980071_2.fastq.bam
zcat BY4741_rep1-GSM1661107/SRR1980052_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep1-GSM1661107/SRR1980052_1.fastq.bam
zcat BY4741_rep1-GSM1661107/SRR1980052_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep1-GSM1661107/SRR1980052_2.fastq.bam
zcat BY4741_rep2-GSM1661108/SRR1980053_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep2-GSM1661108/SRR1980053_1.fastq.bam
zcat BY4741_rep2-GSM1661108/SRR1980053_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep2-GSM1661108/SRR1980053_2.fastq.bam
zcat BY4741_rep3-1-GSM1661109/SRR1980054_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep3-1-GSM1661109/SRR1980054_1.fastq.bam
zcat BY4741_rep3-1-GSM1661109/SRR1980054_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep3-1-GSM1661109/SRR1980054_2.fastq.bam
zcat BY4741_rep3-2-GSM1661110/SRR1980055_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep3-2-GSM1661110/SRR1980055_1.fastq.bam
zcat BY4741_rep3-2-GSM1661110/SRR1980055_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep3-2-GSM1661110/SRR1980055_2.fastq.bam
zcat BY4741_rep5-GSM1661111/SRR1980056_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep5-GSM1661111/SRR1980056_1.fastq.bam
zcat BY4741_rep5-GSM1661111/SRR1980056_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep5-GSM1661111/SRR1980056_2.fastq.bam
zcat BY4741_rep6-2-GSM1661113/SRR1980058_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep6-2-GSM1661113/SRR1980058_1.fastq.bam
zcat BY4741_rep6-2-GSM1661113/SRR1980058_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep6-2-GSM1661113/SRR1980058_2.fastq.bam
zcat BY4741_rep6-GSM1661112/SRR1980057_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep6-GSM1661112/SRR1980057_1.fastq.bam
zcat BY4741_rep6-GSM1661112/SRR1980057_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep6-GSM1661112/SRR1980057_2.fastq.bam
zcat BY4741_rep7-GSM1661114/SRR1980059_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep7-GSM1661114/SRR1980059_1.fastq.bam
zcat BY4741_rep7-GSM1661114/SRR1980059_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep7-GSM1661114/SRR1980059_2.fastq.bam
zcat BY4741_rep8-GSM1661115/SRR1980060_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep8-GSM1661115/SRR1980060_1.fastq.bam
zcat BY4741_rep8-GSM1661115/SRR1980060_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep8-GSM1661115/SRR1980060_2.fastq.bam
zcat BY4741_rep9-2-GSM1661117/SRR1980062_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep9-2-GSM1661117/SRR1980062_1.fastq.bam
zcat BY4741_rep9-2-GSM1661117/SRR1980062_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep9-2-GSM1661117/SRR1980062_2.fastq.bam
zcat BY4741_rep9-GSM1661116/SRR1980061_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep9-GSM1661116/SRR1980061_1.fastq.bam
zcat BY4741_rep9-GSM1661116/SRR1980061_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o BY4741_rep9-GSM1661116/SRR1980061_2.fastq.bam
zcat Diamide_rep1-2-GSM1661131/SRR1980076_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Diamide_rep1-2-GSM1661131/SRR1980076_1.fastq.bam
zcat Diamide_rep1-2-GSM1661131/SRR1980076_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Diamide_rep1-2-GSM1661131/SRR1980076_2.fastq.bam
zcat Diamide_rep1-GSM1661130/SRR1980075_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Diamide_rep1-GSM1661130/SRR1980075_1.fastq.bam
zcat Diamide_rep1-GSM1661130/SRR1980075_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Diamide_rep1-GSM1661130/SRR1980075_2.fastq.bam
zcat Diamide_rep2-GSM1661132/SRR1980077_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Diamide_rep2-GSM1661132/SRR1980077_1.fastq.bam
zcat Diamide_rep2-GSM1661132/SRR1980077_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Diamide_rep2-GSM1661132/SRR1980077_2.fastq.bam
zcat H4d4-14_rep1-2-GSM1661139/SRR1980084_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4d4-14_rep1-2-GSM1661139/SRR1980084_1.fastq.bam
zcat H4d4-14_rep1-2-GSM1661139/SRR1980084_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4d4-14_rep1-2-GSM1661139/SRR1980084_2.fastq.bam
zcat H4d4-14_rep1-GSM1661138/SRR1980083_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4d4-14_rep1-GSM1661138/SRR1980083_1.fastq.bam
zcat H4d4-14_rep1-GSM1661138/SRR1980083_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4d4-14_rep1-GSM1661138/SRR1980083_2.fastq.bam
zcat H4d4-14_rep2-2-GSM1661141/SRR1980086_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4d4-14_rep2-2-GSM1661141/SRR1980086_1.fastq.bam
zcat H4d4-14_rep2-2-GSM1661141/SRR1980086_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4d4-14_rep2-2-GSM1661141/SRR1980086_2.fastq.bam
zcat H4d4-14_rep2-GSM1661140/SRR1980085_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4d4-14_rep2-GSM1661140/SRR1980085_1.fastq.bam
zcat H4d4-14_rep2-GSM1661140/SRR1980085_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4d4-14_rep2-GSM1661140/SRR1980085_2.fastq.bam
zcat H4K16Q_rep1-2-GSM1661143/SRR1980088_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4K16Q_rep1-2-GSM1661143/SRR1980088_1.fastq.bam
zcat H4K16Q_rep1-2-GSM1661143/SRR1980088_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4K16Q_rep1-2-GSM1661143/SRR1980088_2.fastq.bam
zcat H4K16Q_rep1-GSM1661142/SRR1980087_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4K16Q_rep1-GSM1661142/SRR1980087_1.fastq.bam
zcat H4K16Q_rep1-GSM1661142/SRR1980087_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4K16Q_rep1-GSM1661142/SRR1980087_2.fastq.bam
zcat H4Q93E-GSM1661144/SRR1980089_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4Q93E-GSM1661144/SRR1980089_1.fastq.bam
zcat H4Q93E-GSM1661144/SRR1980089_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4Q93E-GSM1661144/SRR1980089_2.fastq.bam
zcat H4R23A_rep1-2-GSM1661146/SRR1980091_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4R23A_rep1-2-GSM1661146/SRR1980091_1.fastq.bam
zcat H4R23A_rep1-2-GSM1661146/SRR1980091_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4R23A_rep1-2-GSM1661146/SRR1980091_2.fastq.bam
zcat H4R23A_rep1-GSM1661145/SRR1980090_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4R23A_rep1-GSM1661145/SRR1980090_1.fastq.bam
zcat H4R23A_rep1-GSM1661145/SRR1980090_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4R23A_rep1-GSM1661145/SRR1980090_2.fastq.bam
zcat H4R23A_rep2-2-GSM1661148/SRR1980093_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4R23A_rep2-2-GSM1661148/SRR1980093_1.fastq.bam
zcat H4R23A_rep2-2-GSM1661148/SRR1980093_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4R23A_rep2-2-GSM1661148/SRR1980093_2.fastq.bam
zcat H4R23A_rep2-GSM1661147/SRR1980092_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4R23A_rep2-GSM1661147/SRR1980092_1.fastq.bam
zcat H4R23A_rep2-GSM1661147/SRR1980092_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4R23A_rep2-GSM1661147/SRR1980092_2.fastq.bam
zcat H4-WT-GSM1661137/SRR1980082_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4-WT-GSM1661137/SRR1980082_1.fastq.bam
zcat H4-WT-GSM1661137/SRR1980082_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o H4-WT-GSM1661137/SRR1980082_2.fastq.bam
zcat med1d_rep1-2-GSM1661150/SRR1980095_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep1-2-GSM1661150/SRR1980095_1.fastq.bam
zcat med1d_rep1-2-GSM1661150/SRR1980095_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep1-2-GSM1661150/SRR1980095_2.fastq.bam
zcat med1d_rep1-GSM1661149/SRR1980094_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep1-GSM1661149/SRR1980094_1.fastq.bam
zcat med1d_rep1-GSM1661149/SRR1980094_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep1-GSM1661149/SRR1980094_2.fastq.bam
zcat med1d_rep2-2-GSM1661152/SRR1980097_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep2-2-GSM1661152/SRR1980097_1.fastq.bam
zcat med1d_rep2-2-GSM1661152/SRR1980097_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep2-2-GSM1661152/SRR1980097_2.fastq.bam
zcat med1d_rep2-GSM1661151/SRR1980096_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep2-GSM1661151/SRR1980096_1.fastq.bam
zcat med1d_rep2-GSM1661151/SRR1980096_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep2-GSM1661151/SRR1980096_2.fastq.bam
zcat med1d_rep3-GSM1661153/SRR1980098_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep3-GSM1661153/SRR1980098_1.fastq.bam
zcat med1d_rep3-GSM1661153/SRR1980098_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o med1d_rep3-GSM1661153/SRR1980098_2.fastq.bam
zcat Mnase-0.25X_Dimer-GSM1661182/SRR1980127_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.25X_Dimer-GSM1661182/SRR1980127_1.fastq.bam
zcat Mnase-0.25X_Dimer-GSM1661182/SRR1980127_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.25X_Dimer-GSM1661182/SRR1980127_2.fastq.bam
zcat Mnase-0.25X_Monomer-GSM1661186/SRR1980131_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.25X_Monomer-GSM1661186/SRR1980131_1.fastq.bam
zcat Mnase-0.25X_Monomer-GSM1661186/SRR1980131_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.25X_Monomer-GSM1661186/SRR1980131_2.fastq.bam
zcat Mnase-0.25X_Small-GSM1661194/SRR1980139_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.25X_Small-GSM1661194/SRR1980139_1.fastq.bam
zcat Mnase-0.25X_Small-GSM1661194/SRR1980139_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.25X_Small-GSM1661194/SRR1980139_2.fastq.bam
zcat Mnase-0.25X_Tri-Tetra-GSM1661190/SRR1980135_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.25X_Tri-Tetra-GSM1661190/SRR1980135_1.fastq.bam
zcat Mnase-0.25X_Tri-Tetra-GSM1661190/SRR1980135_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.25X_Tri-Tetra-GSM1661190/SRR1980135_2.fastq.bam
zcat Mnase-0.5X_Dimer-GSM1661183/SRR1980128_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.5X_Dimer-GSM1661183/SRR1980128_1.fastq.bam
zcat Mnase-0.5X_Dimer-GSM1661183/SRR1980128_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.5X_Dimer-GSM1661183/SRR1980128_2.fastq.bam
zcat Mnase-0.5X_Monomer-GSM1661187/SRR1980132_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.5X_Monomer-GSM1661187/SRR1980132_1.fastq.bam
zcat Mnase-0.5X_Monomer-GSM1661187/SRR1980132_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.5X_Monomer-GSM1661187/SRR1980132_2.fastq.bam
zcat Mnase-0.5X_Small-GSM1661195/SRR1980140_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.5X_Small-GSM1661195/SRR1980140_1.fastq.bam
zcat Mnase-0.5X_Small-GSM1661195/SRR1980140_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.5X_Small-GSM1661195/SRR1980140_2.fastq.bam
zcat Mnase-0.5X_Tri-Tetra-GSM1661191/SRR1980136_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.5X_Tri-Tetra-GSM1661191/SRR1980136_1.fastq.bam
zcat Mnase-0.5X_Tri-Tetra-GSM1661191/SRR1980136_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.5X_Tri-Tetra-GSM1661191/SRR1980136_2.fastq.bam
zcat Mnase-0.75X_Dimer-GSM1661184/SRR1980129_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.75X_Dimer-GSM1661184/SRR1980129_1.fastq.bam
zcat Mnase-0.75X_Dimer-GSM1661184/SRR1980129_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.75X_Dimer-GSM1661184/SRR1980129_2.fastq.bam
zcat Mnase-0.75X_Monomer-GSM1661188/SRR1980133_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.75X_Monomer-GSM1661188/SRR1980133_1.fastq.bam
zcat Mnase-0.75X_Monomer-GSM1661188/SRR1980133_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.75X_Monomer-GSM1661188/SRR1980133_2.fastq.bam
zcat Mnase-0.75X_Small-GSM1661196/SRR1980141_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.75X_Small-GSM1661196/SRR1980141_1.fastq.bam
zcat Mnase-0.75X_Small-GSM1661196/SRR1980141_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.75X_Small-GSM1661196/SRR1980141_2.fastq.bam
zcat Mnase-0.75X_Tri-Tetra-GSM1661192/SRR1980137_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.75X_Tri-Tetra-GSM1661192/SRR1980137_1.fastq.bam
zcat Mnase-0.75X_Tri-Tetra-GSM1661192/SRR1980137_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-0.75X_Tri-Tetra-GSM1661192/SRR1980137_2.fastq.bam
zcat Mnase-1X_Dimer-GSM1661185/SRR1980130_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-1X_Dimer-GSM1661185/SRR1980130_1.fastq.bam
zcat Mnase-1X_Dimer-GSM1661185/SRR1980130_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-1X_Dimer-GSM1661185/SRR1980130_2.fastq.bam
zcat Mnase-1X_Monomer-GSM1661189/SRR1980134_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-1X_Monomer-GSM1661189/SRR1980134_1.fastq.bam
zcat Mnase-1X_Monomer-GSM1661189/SRR1980134_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-1X_Monomer-GSM1661189/SRR1980134_2.fastq.bam
zcat Mnase-1X_Small-GSM1661197/SRR1980142_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-1X_Small-GSM1661197/SRR1980142_1.fastq.bam
zcat Mnase-1X_Small-GSM1661197/SRR1980142_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-1X_Small-GSM1661197/SRR1980142_2.fastq.bam
zcat Mnase-1X_Tri-Tetra-GSM1661193/SRR1980138_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-1X_Tri-Tetra-GSM1661193/SRR1980138_1.fastq.bam
zcat Mnase-1X_Tri-Tetra-GSM1661193/SRR1980138_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Mnase-1X_Tri-Tetra-GSM1661193/SRR1980138_2.fastq.bam
zcat rgr1-100-37C_rep1-GSM1661174/SRR1980119_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rgr1-100-37C_rep1-GSM1661174/SRR1980119_1.fastq.bam
zcat rgr1-100-37C_rep1-GSM1661174/SRR1980119_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rgr1-100-37C_rep1-GSM1661174/SRR1980119_2.fastq.bam
zcat rgr1-100-37C_rep2-GSM1661175/SRR1980120_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rgr1-100-37C_rep2-GSM1661175/SRR1980120_1.fastq.bam
zcat rgr1-100-37C_rep2-GSM1661175/SRR1980120_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rgr1-100-37C_rep2-GSM1661175/SRR1980120_2.fastq.bam
zcat rnh201d_rep1-GSM1661154/SRR1980099_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rnh201d_rep1-GSM1661154/SRR1980099_1.fastq.bam
zcat rnh201d_rep1-GSM1661154/SRR1980099_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rnh201d_rep1-GSM1661154/SRR1980099_2.fastq.bam
zcat rnh201d_rep2-GSM1661155/SRR1980100_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rnh201d_rep2-GSM1661155/SRR1980100_1.fastq.bam
zcat rnh201d_rep2-GSM1661155/SRR1980100_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rnh201d_rep2-GSM1661155/SRR1980100_2.fastq.bam
zcat rpd3d_rep1-2-GSM1661157/SRR1980102_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rpd3d_rep1-2-GSM1661157/SRR1980102_1.fastq.bam
zcat rpd3d_rep1-2-GSM1661157/SRR1980102_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rpd3d_rep1-2-GSM1661157/SRR1980102_2.fastq.bam
zcat rpd3d_rep1-GSM1661156/SRR1980101_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rpd3d_rep1-GSM1661156/SRR1980101_1.fastq.bam
zcat rpd3d_rep1-GSM1661156/SRR1980101_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rpd3d_rep1-GSM1661156/SRR1980101_2.fastq.bam
zcat rpd3d_rep2-GSM1661158/SRR1980103_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rpd3d_rep2-GSM1661158/SRR1980103_1.fastq.bam
zcat rpd3d_rep2-GSM1661158/SRR1980103_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rpd3d_rep2-GSM1661158/SRR1980103_2.fastq.bam
zcat rsc8-21-37C_rep1-GSM1661176/SRR1980121_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rsc8-21-37C_rep1-GSM1661176/SRR1980121_1.fastq.bam
zcat rsc8-21-37C_rep1-GSM1661176/SRR1980121_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rsc8-21-37C_rep1-GSM1661176/SRR1980121_2.fastq.bam
zcat rsc8-21-37C_rep2-GSM1661177/SRR1980122_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rsc8-21-37C_rep2-GSM1661177/SRR1980122_1.fastq.bam
zcat rsc8-21-37C_rep2-GSM1661177/SRR1980122_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rsc8-21-37C_rep2-GSM1661177/SRR1980122_2.fastq.bam
zcat rtt109d_rep1-2-GSM1661160/SRR1980105_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep1-2-GSM1661160/SRR1980105_1.fastq.bam
zcat rtt109d_rep1-2-GSM1661160/SRR1980105_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep1-2-GSM1661160/SRR1980105_2.fastq.bam
zcat rtt109d_rep1-GSM1661159/SRR1980104_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep1-GSM1661159/SRR1980104_1.fastq.bam
zcat rtt109d_rep1-GSM1661159/SRR1980104_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep1-GSM1661159/SRR1980104_2.fastq.bam
zcat rtt109d_rep2-2-GSM1661162/SRR1980107_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep2-2-GSM1661162/SRR1980107_1.fastq.bam
zcat rtt109d_rep2-2-GSM1661162/SRR1980107_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep2-2-GSM1661162/SRR1980107_2.fastq.bam
zcat rtt109d_rep2-GSM1661161/SRR1980106_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep2-GSM1661161/SRR1980106_1.fastq.bam
zcat rtt109d_rep2-GSM1661161/SRR1980106_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep2-GSM1661161/SRR1980106_2.fastq.bam
zcat rtt109d_rep3-GSM1661163/SRR1980108_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep3-GSM1661163/SRR1980108_1.fastq.bam
zcat rtt109d_rep3-GSM1661163/SRR1980108_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o rtt109d_rep3-GSM1661163/SRR1980108_2.fastq.bam
zcat scc2-4-37C_rep1-GSM1661178/SRR1980123_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o scc2-4-37C_rep1-GSM1661178/SRR1980123_1.fastq.bam
zcat scc2-4-37C_rep1-GSM1661178/SRR1980123_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o scc2-4-37C_rep1-GSM1661178/SRR1980123_2.fastq.bam
zcat scc2-4-37C_rep2-GSM1661179/SRR1980124_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o scc2-4-37C_rep2-GSM1661179/SRR1980124_1.fastq.bam
zcat scc2-4-37C_rep2-GSM1661179/SRR1980124_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o scc2-4-37C_rep2-GSM1661179/SRR1980124_2.fastq.bam
zcat ssu72-2_rep1-2-GSM1661165/SRR1980110_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep1-2-GSM1661165/SRR1980110_1.fastq.bam
zcat ssu72-2_rep1-2-GSM1661165/SRR1980110_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep1-2-GSM1661165/SRR1980110_2.fastq.bam
zcat ssu72-2_rep1-GSM1661164/SRR1980109_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep1-GSM1661164/SRR1980109_1.fastq.bam
zcat ssu72-2_rep1-GSM1661164/SRR1980109_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep1-GSM1661164/SRR1980109_2.fastq.bam
zcat ssu72-2_rep2-2-GSM1661167/SRR1980112_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep2-2-GSM1661167/SRR1980112_1.fastq.bam
zcat ssu72-2_rep2-2-GSM1661167/SRR1980112_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep2-2-GSM1661167/SRR1980112_2.fastq.bam
zcat ssu72-2_rep2-GSM1661166/SRR1980111_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep2-GSM1661166/SRR1980111_1.fastq.bam
zcat ssu72-2_rep2-GSM1661166/SRR1980111_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep2-GSM1661166/SRR1980111_2.fastq.bam
zcat ssu72-2_rep3-GSM1661168/SRR1980113_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep3-GSM1661168/SRR1980113_1.fastq.bam
zcat ssu72-2_rep3-GSM1661168/SRR1980113_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o ssu72-2_rep3-GSM1661168/SRR1980113_2.fastq.bam
zcat sth1-2-37C_rep1-GSM1661180/SRR1980125_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o sth1-2-37C_rep1-GSM1661180/SRR1980125_1.fastq.bam
zcat sth1-2-37C_rep1-GSM1661180/SRR1980125_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o sth1-2-37C_rep1-GSM1661180/SRR1980125_2.fastq.bam
zcat sth1-2-37C_rep2-GSM1661181/SRR1980126_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o sth1-2-37C_rep2-GSM1661181/SRR1980126_1.fastq.bam
zcat sth1-2-37C_rep2-GSM1661181/SRR1980126_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o sth1-2-37C_rep2-GSM1661181/SRR1980126_2.fastq.bam
zcat Thiolutin_rep1-GSM1661133/SRR1980078_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Thiolutin_rep1-GSM1661133/SRR1980078_1.fastq.bam
zcat Thiolutin_rep1-GSM1661133/SRR1980078_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Thiolutin_rep1-GSM1661133/SRR1980078_2.fastq.bam
zcat Thiolutin_rep2-GSM1661134/SRR1980079_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Thiolutin_rep2-GSM1661134/SRR1980079_1.fastq.bam
zcat Thiolutin_rep2-GSM1661134/SRR1980079_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o Thiolutin_rep2-GSM1661134/SRR1980079_2.fastq.bam
zcat top1d_rep1-GSM1661169/SRR1980114_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o top1d_rep1-GSM1661169/SRR1980114_1.fastq.bam
zcat top1d_rep1-GSM1661169/SRR1980114_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o top1d_rep1-GSM1661169/SRR1980114_2.fastq.bam
zcat top1d_rep2-GSM1661170/SRR1980115_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o top1d_rep2-GSM1661170/SRR1980115_1.fastq.bam
zcat top1d_rep2-GSM1661170/SRR1980115_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o top1d_rep2-GSM1661170/SRR1980115_2.fastq.bam
zcat W303_rep1-2-GSM1661136/SRR1980081_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o W303_rep1-2-GSM1661136/SRR1980081_1.fastq.bam
zcat W303_rep1-2-GSM1661136/SRR1980081_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o W303_rep1-2-GSM1661136/SRR1980081_2.fastq.bam
zcat W303_rep1-GSM1661135/SRR1980080_1.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o W303_rep1-GSM1661135/SRR1980080_1.fastq.bam
zcat W303_rep1-GSM1661135/SRR1980080_2.fastq.gz | python /oak/stanford/groups/akundaje/marinovg/code/trimfastq.py - 30 -stdout | /oak/stanford/groups/akundaje/marinovg/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3 -p 1 -v 2 -k 2 -m 1 -t --best --strata -q --sam-nh --sam - | /oak/stanford/groups/akundaje/marinovg/programs/samtools-0.1.18/samtools view -bT /oak/stanford/groups/akundaje/marinovg/genomes/sacCer3/bowtie-indexes/sacCer3.fa - -o W303_rep1-GSM1661135/SRR1980080_2.fastq.bam